MIRU-VNTRplus

MIRU-VNTRplus provides genotyping and comparative analysis of Mycobacterium tuberculosis complex (MTBC) strains using multi-locus variable number tandem repeat (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) and complementary typing data for lineage assignment and epidemiological investigation.

Key Features:

• Comprehensive Genotyping Analysis: Integrates MLVA/MIRU data with spoligotype, large sequence polymorphism (LSP), single nucleotide polymorphism (SNP) data and IS6110 restriction fragment length polymorphism (RFLP) for analyses based on individual markers or weighted combinations.
• Reference Database: Includes 186 reference strains representing primary MTBC lineages annotated with geographical origin, drug susceptibility profiles, MIRU-VNTR profiles, spoligotyping patterns, SNP profiles, LSP profiles, and IS6110 RFLP fingerprints.
• Data Exploration Tools: Supports searching for similar strains, constructing phylogenetic trees, building minimum spanning trees, and mapping geographic information for epidemiological context.
• Flexible Data Import and Analysis: Allows analysis of single or multiple strains with lineage identification with or without reference strains, best-match analysis, and tree-based analyses using single or combined marker datasets.
• Genotype Nomenclature: Implements the expanding MLVA MtbC15-9 genotype nomenclature for standardized genotype representation and communication.
• Evaluation and Performance: Database consistency and analysis parameters were evaluated using the reference collection and an external dataset of 629 strains, with lineage predictions from 24-locus MIRU-VNTR combined with spoligotyping achieving verification rates exceeding 99% under optimal conditions.

Scientific Applications:

• Epidemiological Surveillance: Identification and tracking of locally and internationally circulating MTBC clones to support tuberculosis surveillance and disease control.
• Lineage Assignment and Clonal Analysis: High-resolution clonal identification and lineage prediction using 24-locus MIRU-VNTR and combined marker analyses for population and phylogenetic studies.

Methodology:

Performs MLVA analysis targeting MIRU loci, integrates spoligotype, LSP, SNP and IS6110 RFLP data, applies best-match analysis, constructs phylogenetic trees and minimum spanning trees, uses weighted or single-marker datasets for lineage identification, and employs the MLVA MtbC15-9 nomenclature and 24-locus MIRU-VNTR scheme.